Compositions and methods for modifying genomes
First Claim
1. A method of modifying a nucleotide sequence at a target site in the genome of a eukaryotic cell comprising:
- introducing into said eukaryotic cell(i) a DNA-targeting RNA, or a DNA polynucleotide encoding a DNA-targeting RNA, wherein the DNA-targeting RNA comprises;
(a) a first segment comprising a nucleotide sequence that is complementary to a sequence in the target DNA; and
(b) a second segment that interacts with a Csm1 polypeptide; and
(ii) a Csm1 polypeptide, or a polynucleotide encoding a Csm1 polypeptide, wherein the Csm1 polypeptide comprises;
(a) an RNA-binding portion that interacts with the DNA-targeting RNA; and
(b) an activity portion that exhibits site-directed enzymatic activity,wherein said Csm1 polypeptide has at least 95% identity with a sequence selected from the group consisting of;
SEQ ID NOs;
134, 147, 160, and 230, and has Csm1 nuclease activity, wherein said method modifies said nucleotide sequence at said target site, and wherein said genome of a eukaryotic cell is a nuclear, plastid, or mitochondrial genome.
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Abstract
Compositions and methods for modifying genomic DNA sequences are provided. The methods produce double-stranded breaks (DSBs) at pre-determined target sites in a genomic DNA sequence, resulting in mutation, insertion, and/or deletion of DNA sequences at the target site(s) in a genome. Compositions comprise DNA constructs comprising nucleotide sequences that encode a Cpf1 or Csm1 protein operably linked to a promoter that is operable in the cells of interest. The DNA constructs can be used to direct the modification of genomic DNA at pre-determined genomic loci. Methods to use these DNA constructs to modify genomic DNA sequences are described herein. Additionally, compositions and methods for modulating the expression of genes are provided. Compositions comprise DNA constructs comprising a promoter that is operable in the cells of interest operably linked to nucleotide sequences that encode a mutated Cpf1 or Csm1 protein with an abolished ability to produce DSBs, optionally linked to a domain that regulates transcriptional activity. The methods can be used to up- or down-regulate the expression of genes at predetermined genomic loci.
158 Citations
24 Claims
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1. A method of modifying a nucleotide sequence at a target site in the genome of a eukaryotic cell comprising:
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introducing into said eukaryotic cell (i) a DNA-targeting RNA, or a DNA polynucleotide encoding a DNA-targeting RNA, wherein the DNA-targeting RNA comprises;
(a) a first segment comprising a nucleotide sequence that is complementary to a sequence in the target DNA; and
(b) a second segment that interacts with a Csm1 polypeptide; and(ii) a Csm1 polypeptide, or a polynucleotide encoding a Csm1 polypeptide, wherein the Csm1 polypeptide comprises;
(a) an RNA-binding portion that interacts with the DNA-targeting RNA; and
(b) an activity portion that exhibits site-directed enzymatic activity,wherein said Csm1 polypeptide has at least 95% identity with a sequence selected from the group consisting of;
SEQ ID NOs;
134, 147, 160, and 230, and has Csm1 nuclease activity, wherein said method modifies said nucleotide sequence at said target site, and wherein said genome of a eukaryotic cell is a nuclear, plastid, or mitochondrial genome.- View Dependent Claims (3, 4, 5, 7, 9, 10, 16, 17, 20, 22, 24)
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2. A method of modifying a nucleotide sequence at a target site in the genome of a prokaryotic cell comprising:
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introducing into said prokaryotic cell (i) a DNA-targeting RNA, or a DNA polynucleotide encoding a DNA-targeting RNA, wherein the DNA-targeting RNA comprises;
(a) a first segment comprising a nucleotide sequence that is complementary to a sequence in the target DNA; and
(b) a second segment that interacts with a Csm1 polypeptide; and(ii) a Csm1 polypeptide, or a polynucleotide encoding a Csm1 polypeptide, wherein the Csm1 polypeptide comprises;
(a) an RNA-binding portion that interacts with the DNA-targeting RNA; and
(b) an activity portion that exhibits site-directed enzymatic activity,wherein said Csm1 polypeptide has at least 95% identity with a sequence selected from the group consisting of;
SEQ ID NOs;
134, 147, 160, and 230 and has Csm1 nuclease activity, wherein said method modifies said nucleotide sequence at said target site, wherein said genome of a prokaryotic cell is a chromosomal, plasmid, or other intracellular DNA sequence, and wherein said prokaryotic cell is not the natural host of a gene encoding said Csm1 polypeptide.- View Dependent Claims (6, 8)
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11. A nucleic acid molecule comprising a polynucleotide sequence encoding a Csm1 polypeptide, wherein said polynucleotide sequence has at least 95% identity with a sequence selected from the group consisting of SEQ ID NOs:
- 185, 186, and 193, or a fragment or variant thereof, or wherein said polynucleotide sequence encodes a Csm1 polypeptide with at least 95% identity to a sequence selected from the group consisting of SEQ ID NOs;
134, 147, 160, and 230 and has Csm1 nuclease activity, and wherein said polynucleotide sequence encoding a Csm1 polypeptide is operably linked to a promoter that is heterologous to the polynucleotide sequence encoding a Csm1 polypeptide. - View Dependent Claims (12, 13, 14, 15, 18, 19, 21, 23)
- 185, 186, and 193, or a fragment or variant thereof, or wherein said polynucleotide sequence encodes a Csm1 polypeptide with at least 95% identity to a sequence selected from the group consisting of SEQ ID NOs;
Specification